Karakalpakstan has quite a rich biodiversity represented by 498 vertebrate species, including 68 mammals, 307 birds, 33 reptiles, two amphibians, and 49 fish.

Karakalpakstan fauna has its own peculiarities. Desert inhabitants are considered the best runners. For instance, hedgehogs, which are relatively slowmoving animals, are represented here by eared and Brandt's hedgehogs, which have considerably longer limbs than European varieties.

The most widely distributed mammals in Karakalpakstan include long-clawed ground squirrels, jerboas, wolves, wild boars, foxes and hares. Birds are represented by saxaul jays, desert sparrows and magpies. The most commonly encountered reptiles are lizards and sand boas. The fish species include grass carp, Amudarya trout, carp, pike perch, snakehead, silver carp and others.

The number of invertebrate species is seven times greater than that of vertebrates. The most common invertebrates include phalanges, scorpions, tarantulas and beetles. It is worth noting that Karakalpakstan is known for its large variety of insect species – 1,392.

In recent decades, the number of animal species has declined considerably. Sixtythree species have gained protection according to the Red Book of Uzbekistan (2003). The famous Asiatic cheetah and Turan tiger were added to the Red List of International Union for Conservation of Nature (IUCN) as an extinct mammal species. Mammals such as honey badger, Turkmen caracal, Turkmen onager, and Ustyurt sheep are included on the IUCN critically endangered list. The IUCN list also contains several endangered birds (marbled teal, Asiatic white crane and others) as well as various fish species (large and small Amudarya shovelnose and others).